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- PDB-8qlx: Magnaporthe grisea Woronin Body Major protein crystallized in cellulo -

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Basic information

Entry
Database: PDB / ID: 8qlx
TitleMagnaporthe grisea Woronin Body Major protein crystallized in cellulo
ComponentsPutative vacuolar ATPase MVP1
KeywordsSTRUCTURAL PROTEIN / self-assembly / natively crystallizing / HEX-1 / Woronin Body Major Protein
Function / homology
Function and homology information


positive regulation of translational elongation / translation elongation factor activity / ribosome binding / RNA binding
Similarity search - Function
Hex1, S1 domain / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor IF5A-like / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Putative vacuolar ATPase MVP1
Similarity search - Component
Biological speciesPyricularia grisea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBoger, J. / Redecke, L.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research05K18FLA Germany
CitationJournal: To Be Published
Title: Magnaporthe grisea Woronin Body Major protein crystallized in cellulo
Authors: Boger, J. / Redecke, L.
History
DepositionSep 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative vacuolar ATPase MVP1


Theoretical massNumber of molelcules
Total (without water)20,0081
Polymers20,0081
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.660, 57.660, 187.890
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-264-

HOH

21A-283-

HOH

31A-293-

HOH

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Components

#1: Protein Putative vacuolar ATPase MVP1 / Vacuolar-ATPase


Mass: 20007.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyricularia grisea (fungus) / Gene: VATP / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UW16
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 300 K / Method: in cell
Details: spontaneous in cellulo crystallization inside living T. ni (High Five cells) after recombinant expression using the DH10EmBacY baculovirus system

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→93.95 Å / Num. obs: 18144 / % possible obs: 100 % / Redundancy: 176.9 % / Biso Wilson estimate: 25.69 Å2 / CC1/2: 0.9993 / Net I/σ(I): 25.86
Reflection shellResolution: 1.8→1.82 Å / Num. unique obs: 855 / CC1/2: 0.2583
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49.94 Å / SU ML: 0.2406 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.1562
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2363 1401 8.12 %
Rwork0.2123 15855 -
obs0.2142 17256 95.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.54 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1033 0 0 93 1126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00851047
X-RAY DIFFRACTIONf_angle_d1.05121417
X-RAY DIFFRACTIONf_chiral_restr0.0761172
X-RAY DIFFRACTIONf_plane_restr0.0081181
X-RAY DIFFRACTIONf_dihedral_angle_d6.1134146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.4781080.41821214X-RAY DIFFRACTION75.89
1.86-1.940.35011240.31611404X-RAY DIFFRACTION87.97
1.94-2.030.25861330.25161539X-RAY DIFFRACTION94.52
2.03-2.130.24351390.21681587X-RAY DIFFRACTION97.46
2.13-2.270.23571430.19531603X-RAY DIFFRACTION98.87
2.27-2.440.23571450.18891632X-RAY DIFFRACTION99.89
2.44-2.690.24461480.20411649X-RAY DIFFRACTION99.72
2.69-3.080.22711480.20511664X-RAY DIFFRACTION99.89
3.08-3.880.1891520.19321709X-RAY DIFFRACTION100
3.88-49.940.23491610.2041854X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.832797752830.7618811700411.075913248624.96704706538-0.7360243639374.639520231-0.1030238085570.202072020162-0.438961310579-0.2152523255890.04581359935110.6178300913930.314252680756-0.2306532528390.206038575820.4607149428150.123668929312-0.05969345037090.463685337841-0.02687848243890.56715387012815.737581097821.599380856989.3216581391
23.03893894871-0.7059542350470.5408058557263.429103293520.2284560531335.591485258680.0709855002924-0.01222002654980.2449620699730.0432153876022-0.1217718576450.00153858353017-0.008721811609450.07892166274540.05040058855120.15830219865-0.01153746219380.0006942291329980.10078348494-0.02048070160660.2105251978468.4434106222543.391391176187.7894994712
39.288157695781.3793374552-0.5515560019515.00184360939-0.8758317819353.342568909690.185994493262-0.0587369514594-0.746392477986-0.0403921711271-0.247002211407-0.165940329912-0.15600053867-0.2545093303760.09593465847130.5142417602050.191028340768-0.02419571379030.449566622085-0.00577108142760.41242025110723.34901326121.107919238292.7145992853
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 139 through 175 )139 - 175105 - 139
22chain 'A' and (resid 36 through 108 )36 - 1082 - 74
33chain 'A' and (resid 109 through 138 )109 - 13875 - 104

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